9J9D | pdb_00009j9d

Crystal structure of ALK5 kinase domain in complex with inhibitor HM-279

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WOU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	20-25% PEG8000, 0.2 M Na acetate, 0.1 M Tris-HCl pH8.5

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.455	α = 90
b = 75.677	β = 90
c = 89.625	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2023-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.900	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.337	50	99.2	0.998	12.6	3.52		66655

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.337	1.42			0.727

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2WOU	1.337	44.813	65785	3290	99.516	0.191	0.1903	0.1997	0.2089	0.2202	12.503

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.001			0.003		-0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.311
r_dihedral_angle_4_deg	13.352
r_dihedral_angle_3_deg	10.77
r_dihedral_angle_1_deg	6.626
r_lrange_it	2.684
r_lrange_other	2.603
r_angle_other_deg	1.224
r_angle_refined_deg	1.203
r_mcangle_it	1.054
r_mcangle_other	1.053
r_scangle_it	1.046
r_scangle_other	1.046
r_scbond_it	0.634
r_scbond_other	0.634
r_mcbond_it	0.583
r_mcbond_other	0.583
r_nbd_refined	0.193
r_symmetry_nbd_other	0.168
r_nbtor_refined	0.154
r_nbd_other	0.145
r_symmetry_xyhbond_nbd_refined	0.132
r_symmetry_nbd_refined	0.129
r_xyhbond_nbd_refined	0.095
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.053
r_dihedral_angle_other_2_deg	0.012
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2351
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing